I've reffed a bunch too (still do a masked gimmick for one promotion I work for, as I used to do double duty as ref/wrestler). All the points above are great, in addition:
I hate refs who think they're hot shit, "I don't need to know the finish, I'll just count the 3 when it's the 3" etc. The way I did it was to go up to the guys about 30 minutes before they were on and ask "Hey guys, I'm reffing your match tonight, do your know your finish yet? Also is there anything else I need to know?" Don't be a brown-noser, just act professional.
As far as invisibility goes, try and form a triangle with the guys in the ring.
Keep your wits about you with positioning, don't be the ref that stands in the corner as a guy is getting whipped into it.
Bring a watch, then drop timehints when you're checking on guys "CAN YOU CONTINUE??? five mins in guys, five mins DO YOU WANT TO SUBMIT??"
On that note, work on voice levels for shit you want the crowd to hear, and shit you only want the workers to hear. Just like how guys call spots.
Signal everything to the crowd, and to the timekeeper. When there was a near fall I would shoot my hand up with 2 fingers and shout it was a 2-count as loud as I could, then signalled it to the timekeeper. Makes it seem more legit.
Workers will try to use you to communicate to their opponents, do it subtlely.
Also, screw black sneakers. I wore black suit trousers (cheap ones), and black dress shoes/black wrestling boots when I reffed.